Addressing Research Needs in the Field of Plant Virus Ecology by Defining Knowledge Gaps and Developing Wild Dicot Study Systems

Shates, Tessa; Sun, Penglin; Malmström, Carolyn M.; Dominguez, Chrysalyn; Mauck, Kerry E.

doi:10.3389/fmicb.2018.03305

Cited by 38 publications

(32 citation statements)

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“…This knowledge gap can only be addressed by increasing efforts to perform diagnostic and genetic characterization studies using historical specimens and sampling in unmanaged habitats 5,11 . Such approaches are yielding a wealth of information on the diversity and epidemiology of other plant pathogen taxa across different landscape types 5,7,[12][13][14][15][16] . However, to date there have been no efforts to discover and characterize Ca.…”

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confidence: 99%

New Ca. Liberibacter psyllaurous haplotype resurrected from a 49-year-old specimen of Solanum umbelliferum: a native host of the psyllid vector

Mauck

Sun

Meduri

et al. 2019

Sci Rep

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Over the last century, repeated emergence events within the Candidatus Liberibacter taxon have produced pathogens with devastating effects. Presently, our knowledge of Ca. Liberibacter diversity, host associations, and interactions with vectors is limited due to a focus on studying this taxon within crops. But to understand traits associated with pathogen emergence it is essential to study pathogen diversity in wild vegetation as well. Here, we explore historical native host plant associations and diversity of the cosmopolitan species, Ca. L. psyllaurous, also known as Ca. L. solanacearum, which is associated with psyllid yellows disease and zebra chip disease, especially in potato. We screened tissue from herbarium samples of three native solanaceous plants collected near potato-growing regions throughout Southern California over the last century. This screening revealed a new haplotype of Ca. L. psyllaurous (G), which, based on our sampling, has been present in the U.S. since at least 1970. Phylogenetic analysis of this new haplotype suggests that it may be closely related to a newly emerged North American haplotype (F) associated with zebra chip disease in potatoes. Our results demonstrate the value of herbarium sampling for discovering novel Ca. Liberibacter haplotypes not previously associated with disease in crops. Plant pathogen emergence is a major threat to food security 1 and occurs through multiple, non-mutually exclusive pathways 2. For example, a plant pathogen may be a previously unknown or undetected organism, or an organism that was once non-pathogenic to its host but has evolved pathogenic traits over time. Alternatively, the plant pathogen may already be known, but has spread to, and proliferated within, a new geographic area or host population. An outbreak may also represent the re-emergence of a plant pathogen whose incidence had declined significantly in the past but, more recently, increased over a short period. These pathways of disease emergence are complex, and thus require consideration of microbe-plant interactions in both managed and unmanaged systems. With advances in sequencing technologies and development of methods to overcome detection challenges in non-crop hosts 3 , inclusion of wild vegetation in microbial diversity and pathogenicity studies is enabling the discovery and characterization of novel strain types 4 , and expanding our understanding of the processes underlying pathogen emergence 5-8. Among plant pathogens that have emerged as serious threats to food production in the last 100 years are those within the taxon 'Candidatus'(Ca.) Liberibacter 9 (Fig. 1). Ca. Liberibacter species are largely unculturable members of the Alphaproteobacteria class in the Proteobacteria phylum 10. Over the last decade, eight species of Ca. Liberibacter have been identified around the world following emergence as phloem-limited plant pathogens in mostly crop systems (cited within Fig. 1). Each known Ca. Liberibacter species is also associated with one or more herbivorous insect hosts (psyllid...

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mentioning

confidence: 99%

New Ca. Liberibacter psyllaurous haplotype resurrected from a 49-year-old specimen of Solanum umbelliferum: a native host of the psyllid vector

Mauck

Sun

Meduri

et al. 2019

Sci Rep

Self Cite

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“…Wild plants are often latently infected with viruses in nature without any apparent disease symptoms (Min et al, 2012; Shates et al, 2019). Table 1 is a list of plant viruses that are reported to latently infect primary wild host plants and to transition from latency to activation in crops or experimental host plants with the appearance of disease symptoms.…”

Section: Plant Viruses That Can Perform Latent Infectionmentioning

confidence: 99%

Virus Latency and the Impact on Plants

et al. 2019

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Plant viruses are thought to be essentially harmful to the lives of their cultivated crop hosts. In most cases studied, the interaction between viruses and cultivated crop plants negatively affects host morphology and physiology, thereby resulting in disease. Native wild/non-cultivated plants are often latently infected with viruses without any clear symptoms. Although seemingly non-harmful, these viruses pose a threat to cultivated crops because they can be transmitted by vectors and cause disease. Reports are accumulating on infections with latent plant viruses that do not cause disease but rather seem to be beneficial to the lives of wild host plants. In a few cases, viral latency involves the integration of full-length genome copies into the host genome that, in response to environmental stress or during certain developmental stages of host plants, can become activated to generate and replicate episomal copies, a transition from latency to reactivation and causation of disease development. The interaction between viruses and host plants may also lead to the integration of partial-length segments of viral DNA genomes or copy DNA of viral RNA genome sequences into the host genome. Transcripts derived from such integrated viral elements (EVEs) may be beneficial to host plants, for example, by conferring levels of virus resistance and/or causing persistence/latency of viral infections. Studies on viral latency in wild host plants might help us to understand and elucidate the underlying mechanisms of latency and provide insights into the raison d’être for viruses in the lives of plants.

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“…Nevertheless, it was just in the recent decade that plant virologists started to explore more intensively the diversity of viruses in wild ecosystems. Plant virus ecology and epidemiology include studies on viruses infecting weeds and other wild plants (Malmstrom and Alexander, 2016;Shates et al, 2019) as well as water as potential channel for plant virus spread (Mehle and Ravnikar, 2012). In this context, HTS is a well-suited tool, which allows generic investigation of viromes in a diverse set of sample matrices, from an array of different plant species to environmental samples, such as water and soil.…”

Section: Post-discovery Characterization Of New Tomato Virusesmentioning

confidence: 99%

Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing

et al. 2021

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Viruses cause a big fraction of economically important diseases in major crops, including tomato. In the past decade (2011–2020), many emerging or re-emerging tomato-infecting viruses were reported worldwide. In this period, 45 novel viral species were identified in tomato, 14 of which were discovered using high-throughput sequencing (HTS). In this review, we first discuss the role of HTS in these discoveries and its general impact on tomato virome research. We observed that the rate of tomato virus discovery is accelerating in the past few years due to the use of HTS. However, the extent of the post-discovery characterization of viruses is lagging behind and is greater for economically devastating viruses, such as the recently emerged tomato brown rugose fruit virus. Moreover, many known viruses still cause significant economic damages to tomato production. The review of databases and literature revealed at least 312 virus, satellite virus, or viroid species (in 22 families and 39 genera) associated with tomato, which is likely the highest number recorded for any plant. Among those, here, we summarize the current knowledge on the biology, global distribution, and epidemiology of the most important species. Increasing knowledge on tomato virome and employment of HTS to also study viromes of surrounding wild plants and environmental samples are bringing new insights into the understanding of epidemiology and ecology of tomato-infecting viruses and can, in the future, facilitate virus disease forecasting and prevention of virus disease outbreaks in tomato.

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Addressing Research Needs in the Field of Plant Virus Ecology by Defining Knowledge Gaps and Developing Wild Dicot Study Systems

Cited by 38 publications

References 50 publications

New Ca. Liberibacter psyllaurous haplotype resurrected from a 49-year-old specimen of Solanum umbelliferum: a native host of the psyllid vector

New Ca. Liberibacter psyllaurous haplotype resurrected from a 49-year-old specimen of Solanum umbelliferum: a native host of the psyllid vector

Virus Latency and the Impact on Plants

Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing

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